Influenzavirus non-structural protein NS1 is involved in several steps of the virus replication cycle. It counteracts the interferon response, and also exhibits other activities towards viral and cellular RNAs. NS1 is known to bind non-specifically to double-stranded RNA (dsRNA) as well as to viral and cellular RNAs. We set out to search whether NS1 could preferentially bind sequence-specific RNA patterns, and performed an in vitro selection (SELEX) to isolate NS1-specific aptamers from a pool of 80-nucleotide(nt)-long RNAs. Among the 6 families characterized, 3 at least harbour RNA motifs that are highly conserved in viral (+)strand RNAs. An in-depth analysis of the interaction, combining gel-shift assays and fluorimetry (fluorescence anisotropy ; protein-induced fluorescence enhancement), reveals that NS1’s RNA-binding domain (RBD) strongly binds to virus-specific motifs, which suggests that NS1 exerts specific and previously unsuspected activities towards viral RNAs.)